Are Planaria Individuals? What Regenerative Biology is Telling Us About the Nature of Multicellularity

A Variational Synthesis of Evolutionary and Developmental Dynamics

This paper introduces a variational formulation of natural selection, paying special attention to the nature of 'things' and the way that different 'kinds' of 'things' are individuated from-and influence-each other. We use the Bayesian mechanics of particular partitions to understand how slow phylogenetic processes constrain-and are constrained by-fast, phenotypic processes. The main result is a formulation of adaptive fitness as a path integral of phenotypic fitness. Paths of least action, at the phenotypic and phylogenetic scales, can then be read as inference and learning processes, respectively. In this view, a phenotype actively infers the state of its econiche under a generative model, whose parameters are learned via natural (Bayesian model) selection. The ensuing variational synthesis features some unexpected aspects. Perhaps the most notable is that it is not possible to describe or model a population of conspecifics per se. Rather, it is necessary to consider populations of distinct natural kinds that influence each other. This paper is limited to a description of the mathematical apparatus and accompanying ideas. Subsequent work will use these methods for simulations and numerical analyses-and identify points of contact with related mathematical formulations of evolution.

Tissue homeostasis in sponges: Quantitative analysis of cell proliferation and apoptosis

Tissues of multicellular animals are maintained due to a tight balance between cell proliferation and programmed cell death. Sponges are early branching metazoans essential to understanding the key mechanisms of tissue homeostasis. This article is dedicated to the comparative analysis of proliferation and apoptosis in intact tissues of two sponges, Halisarca dujardinii (class Demospongiae) and Leucosolenia variabilis (class Calcarea). Labeled nucleotides EdU and anti-phosphorylated histone 3 antibodies reveal a considerable number of cycling cells in intact tissues of both species. Quantitative DNA staining reveals the classic cell cycle distribution curve. The main type of cycling cells are choanocytes - flagellated cells of the aquiferous system. The rate of proliferation remains constant throughout various areas of sponge bodies that contain choanocytes. The EdU tracking experiments conducted in H. dujardinii indicate that choanocytes may give rise to mesohyl cells through migration. The number of apoptotic cells in tissues of both species is insignificant, although being comparable to the renewing tissues of other animals. In vivo studies with tetramethylrhodamine ethyl ester and CellEvent Caspase-3/7 indicate that apoptosis might be independent of mitochondrial outer membrane permeabilization. Altogether, a combination of confocal laser scanning microscopy and flow cytometry provides a quantitative description of cell proliferation and apoptosis in sponges displaying either rapid growth or cell turnover.

Endless forms most beautiful 2.0: teleonomy and the bioengineering of chimaeric and synthetic organisms

The rich variety of biological forms and behaviours results from one evolutionary history on Earth, via frozen accidents and selection in specific environments. This ubiquitous baggage in natural, familiar model species obscures the plasticity and swarm intelligence of cellular collectives. Significant gaps exist in our understanding of the origin of anatomical novelty, of the relationship between genome and form, and of strategies for control of large-scale structure and function in regenerative medicine and bioengineering. Analysis of living forms that have never existed before is necessary to reveal deep design principles of life as it can be. We briefly review existing examples of chimaeras, cyborgs, hybrots and other beings along the spectrum containing evolved and designed systems. To drive experimental progress in multicellular synthetic morphology, we propose teleonomic (goal-seeking, problem-solving) behaviour in diverse problem spaces as a powerful invariant across possible beings regardless of composition or origin. Cybernetic perspectives on chimaeric morphogenesis erase artificial distinctions established by past limitations of technology and imagination. We suggest that a multi-scale competency architecture facilitates evolution of robust problem-solving, living machines. Creation and analysis of novel living forms will be an essential testbed for the emerging field of diverse intelligence, with numerous implications across regenerative medicine, robotics and ethics.

Multi-scale Chimerism: An experimental window on the algorithms of anatomical control

Despite the immense progress in genetics and cell biology, major knowledge gaps remain with respect to prediction and control of the global morphologies that will result from the cooperation of cells with known genomes. The understanding of cooperativity, competition, and synergy across diverse biological scales has been obscured by a focus on standard model systems that exhibit invariant species-specific anatomies. Morphogenesis of chimeric biological material is an especially instructive window on the control of biological growth and form because it emphasizes the need for prediction without reliance on familiar, standard outcomes. Here, we review an important and fascinating body of data from experiments utilizing DNA transfer, cell transplantation, organ grafting, and parabiosis. We suggest that these are all instances (at different levels of organization) of one general phenomenon: chimerism. Multi-scale chimeras are a powerful conceptual and experimental tool with which to probe the mapping between properties of components and large-scale anatomy: the laws of morphogenesis. The existing data and future advances in this field will impact not only the understanding of cooperation and the evolution of body forms, but also the design of strategies for system-level outcomes in regenerative medicine and swarm robotics.

Metabolic cost of development, regeneration, and reproduction in the planarian Schmidtea mediterranea

Planaria are known for their ability to completely regenerate upon fissioning or experimental amputation. Yet, metabolic costs of regeneration have not been directly measured in planaria. Our goal was to establish the relationships between oxygen consumption (V̇O2), regeneration, and reproductive mode for asexual and sexual strains of Schmidtea mediterranea. We hypothesized that V̇O₂ would vary by regeneration day for both sexual and asexual S. mediterranea, reflecting different costs of tissue reconstruction, but with an additional cost for regenerating sexual organs. Testes regeneration and body mass, as indicators of regeneration progress, and routine mass-specific V̇O₂ as a function of maturity, regeneration, and reproductive mode, were measured over a 22-day regeneration period. Testes growth was highest in sexually mature adults, ~1/2 that in 14-day post-amputation sexual adults, and not detectable in juveniles and hatchlings. Mass-specific routine V̇O₂ in sexuals was highest in mature controls at ~23 μl O₂/g/h, but only half that in juveniles, hatchlings, and 14 day post-amputation adults. Both intact and 14-day post-amputation asexuals had a mass-specific routine V̇O₂ of ~10-12 μl O₂/g/h. The sum of V̇O₂ of all amputated sections was ~100% higher than pre-amputation levels in the first 6 days of regeneration in asexuals, but not sexuals. There was no significant difference in V̇O₂ of head, middle, and tail sections during regeneration. Overall, the highest metabolic costs associated with regeneration occurred during the initial 1-6 days of regeneration in both strains, but regeneration costs for sexual structures were not reflected in major V̇O₂ differences between sexual and asexual strains.

A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape

Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long‐lived, lineage‐restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ‐restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by ‘stemness’ gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ‐cell markers, but often lack germ‐line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole‐body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the ‘wobbling Penrose’ landscape. Here, totipotent ASCs adopt ascending/descending courses of an ‘Escherian stairwell’, in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.

Stem cells of aquatic invertebrates as an advanced tool for assessing ecotoxicological impacts

Environmental stressors are assessed through methods that quantify their impacts on a wide range of metrics including species density, growth rates, reproduction, behaviour and physiology, as on host-pathogen interactions and immunocompetence. Environmental stress may induce additional sublethal effects, like mutations and epigenetic signatures affecting offspring via germline mediated transgenerational inheritance, shaping phenotypic plasticity, increasing disease susceptibility, tissue pathologies, changes in social behaviour and biological invasions. The growing diversity of pollutants released into aquatic environments requires the development of a reliable, standardised and 3R (replacement, reduction and refinement of animals in research) compliant in vitro toolbox. The tools have to be in line with REACH regulation 1907/2006/EC, aiming to improve strategies for potential ecotoxicological risks assessment and monitoring of chemicals threatening human health and aquatic environments. Aquatic invertebrates' adult stem cells (ASCs) are numerous and can be pluripotent, as illustrated by high regeneration ability documented in many of these taxa. This is of further importance as in many aquatic invertebrate taxa, ASCs are able to differentiate into germ cells. Here we propose that ASCs from key aquatic invertebrates may be harnessed for applicable and standardised new tests in ecotoxicology. As part of this approach, a battery of modern techniques and endpoints are proposed to be tested for their ability to correctly identify environmental stresses posed by emerging contaminants in aquatic environments. Consequently, we briefly describe the current status of the available toxicity testing and biota-based monitoring strategies in aquatic environmental ecotoxicology and highlight some of the associated open issues such as replicability, consistency and reliability in the outcomes, for understanding and assessing the impacts of various chemicals on organisms and on the entire aquatic environment. Following this, we describe the benefits of aquatic invertebrate ASC-based tools for better addressing ecotoxicological questions, along with the current obstacles and possible overhaul approaches.

Living Things Are Not (20th Century) Machines: Updating Mechanism Metaphors in Light of the Modern Science of Machine Behavior

One of the most useful metaphors for driving scientific and engineering progress has been that of the “machine.” Much controversy exists about the applicability of this concept in the life sciences. Advances in molecular biology have revealed numerous design principles that can be harnessed to understand cells from an engineering perspective, and build novel devices to rationally exploit the laws of chemistry, physics, and computation. At the same time, organicists point to the many unique features of life, especially at larger scales of organization, which have resisted decomposition analysis and artificial implementation. Here, we argue that much of this debate has focused on inessential aspects of machines – classical properties which have been surpassed by advances in modern Machine Behavior and no longer apply. This emerging multidisciplinary field, at the interface of artificial life, machine learning, and synthetic bioengineering, is highlighting the inadequacy of existing definitions. Key terms such as machine, robot, program, software, evolved, designed, etc., need to be revised in light of technological and theoretical advances that have moved past the dated philosophical conceptions that have limited our understanding of both evolved and designed systems. Moving beyond contingent aspects of historical and current machines will enable conceptual tools that embrace inevitable advances in synthetic and hybrid bioengineering and computer science, toward a framework that identifies essential distinctions between fundamental concepts of devices and living agents. Progress in both theory and practical applications requires the establishment of a novel conception of “machines as they could be,” based on the profound lessons of biology at all scales. We sketch a perspective that acknowledges the remarkable, unique aspects of life to help re-define key terms, and identify deep, essential features of concepts for a future in which sharp boundaries between evolved and designed systems will not exist.

Why isn't sex optional? Stem-cell competition, loss of regenerative capacity, and cancer in metazoan evolution

Animals that can reproduce vegetatively by fission or budding and also sexually via specialized gametes are found in all five primary animal lineages (Bilateria, Cnidaria, Ctenophora, Placozoa, Porifera). Many bilaterian lineages, including roundworms, insects, and most chordates, have lost the capability of vegetative reproduction and are obligately gametic. We suggest a developmental explanation for this evolutionary phenomenon: obligate gametic reproduction is the result of germline stem cells winning a winner-take-all competition with non-germline stem cells for control of reproduction and hence lineage survival. We develop this suggestion by extending Hamilton's rule, which factors the relatedness between parties into the cost/benefit analysis that underpins cooperative behaviors, to include similarity of cellular state. We show how coercive or deceptive cell-cell signaling can be used to make costly cooperative behaviors appear less costly to the cooperating party. We then show how competition between stem-cell lineages can render an ancestral combination of vegetative reproduction with facultative sex unstable, with one or the other process driven to extinction. The increased susceptibility to cancer observed in obligately-sexual lineages is, we suggest, a side-effect of deceptive signaling that is exacerbated by the loss of whole-body regenerative abilities. We suggest a variety of experimental approaches for testing our predictions.

Life, death, and self: Fundamental questions of primitive cognition viewed through the lens of body plasticity and synthetic organisms

Central to the study of cognition is being able to specify the Subject that is making decisions and owning memories and preferences. However, all real cognitive agents are made of parts (such as brains made of cells). The integration of many active subunits into a coherent Self appearing at a larger scale of organization is one of the fundamental questions of evolutionary cognitive science. Typical biological model systems, whether basal or advanced, have a static anatomical structure which obscures important aspects of the mind-body relationship. Recent advances in bioengineering now make it possible to assemble, disassemble, and recombine biological structures at the cell, organ, and whole organism levels. Regenerative biology and controlled chimerism reveal that studies of cognition in intact, "standard", evolved animal bodies are just a narrow slice of a much bigger and as-yet largely unexplored reality: the incredible plasticity of dynamic morphogenesis of biological forms that house and support diverse types of cognition. The ability to produce living organisms in novel configurations makes clear that traditional concepts, such as body, organism, genetic lineage, death, and memory are not as well-defined as commonly thought, and need considerable revision to account for the possible spectrum of living entities. Here, I review fascinating examples of experimental biology illustrating that the boundaries demarcating somatic and cognitive Selves are fluid, providing an opportunity to sharpen inquiries about how evolution exploits physical forces for multi-scale cognition. Developmental (pre-neural) bioelectricity contributes a novel perspective on how the dynamic control of growth and form of the body evolved into sophisticated cognitive capabilities. Most importantly, the development of functional biobots - synthetic living machines with behavioral capacity - provides a roadmap for greatly expanding our understanding of the origin and capacities of cognition in all of its possible material implementations, especially those that emerge de novo, with no lengthy evolutionary history of matching behavioral programs to bodyplan. Viewing fundamental questions through the lens of new, constructed living forms will have diverse impacts, not only in basic evolutionary biology and cognitive science, but also in regenerative medicine of the brain and in artificial intelligence.

Scale-Free Biology: Integrating Evolutionary and Developmental Thinking

When the history of life on earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life on earth can also be seen as the development of life on earth. Here, in reviewing this field, some potentially fruitful research directions suggested by this change in perspective are highlighted. Variation and selection become, for example, bidirectional information flows between scales, while the notions of "cooperation" and "competition" become scale relative. The language of communication, inference, and information processing becomes more useful than the language of causation to describe the interactions of both homogeneous and heterogeneous living systems at any scale. Emerging scale-free theoretical frameworks such as predictive coding and active inference provide conceptual tools for reconceptualizing biology as the study of a unified, multiscale dynamical system.

Does regeneration recapitulate phylogeny? Planaria as a model of body-axis specification in ancestral eumetazoa

Metazoan body plans combine well-defined primary, secondary, and in many bilaterians, tertiary body axes with structural asymmetries at multiple scales. Despite decades of study, how axis-defining symmetries and system-defining asymmetries co-emerge during both evolution and development remain open questions. Regeneration studies in asexual planaria have demonstrated an array of viable forms with symmetrized and, in some cases, duplicated body axes. We suggest that such forms may point toward an ancestral eumetazoan form with characteristics of both cnidarians and placazoa.

Somatic multicellularity as a satisficing solution to the prediction-error minimization problem

Adaptive success in the biosphere requires the dynamic ability to adjust physiological, transcriptional, and behavioral responses to environmental conditions. From chemical networks to organisms to whole communities, biological entities at all levels of organization seek to optimize their predictive power. Here, we argue that this fundamental drive provides a novel perspective on the origin of multicellularity. One way for unicellular organisms to minimize surprise with respect to external inputs is to be surrounded by reproductively-disabled, i.e. somatic copies of themselves - highly predictable agents which in effect reduce uncertainty in their microenvironments. We show that the transition to multicellularity can be modeled as a phase transition driven by environmental threats. We present modeling results showing how multicellular bodies can arise if non-reproductive somatic cells protect their reproductive parents from environmental lethality. We discuss how a somatic body can be interpreted as a Markov blanket around one or more reproductive cells, and how the transition to somatic multicellularity can be represented as a transition from exposure of reproductive cells to a high-uncertainty environment to their protection from environmental uncertainty by this Markov blanket. This is, effectively, a transition by the Markov blanket from transparency to opacity for the variational free energy of the environment. We suggest that the ability to arrest the cell cycle of daughter cells and redirect their resource utilization from division to environmental threat amelioration is the key innovation of obligate multicellular eukaryotes, that the nervous system evolved to exercise this control over long distances, and that cancer is an escape by somatic cells from the control of reproductive cells. Our quantitative model illustrates the evolutionary dynamics of this system, provides a novel hypothesis for the origin of multicellular animal bodies, and suggests a fundamental link between the architectures of complex organisms and information processing in proto-cognitive cellular agents.

Does resource availability help determine the evolutionary route to multicellularity?

Genetic heterogeneity and homogeneity are associated with distinct sets of adaptive advantages and bottlenecks, both in developmental biology and population genetics. Whereas populations of individuals are usually genetically heterogeneous, most multicellular metazoans are genetically homogeneous. Observing that resource scarcity fuels genetic heterogeneity in populations, we propose that monoclonal development is compatible with the resource‐rich and stable internal environments that complex multicellular bodies offer. In turn, polyclonal development persists in tumors and in certain metazoans, both exhibiting a closer dependence on external resources. This eco‐evo‐devo approach also suggests that multicellularity may originally have emerged through polyclonal development in early metazoans, because of their reduced shielding from environmental fluctuations.

Sciences of Observation

Multiple sciences have converged, in the past two decades, on a hitherto mostly unremarked question: what is observation? Here, I examine this evolution, focusing on three sciences: physics, especially quantum information theory, developmental biology, especially its molecular and “evo-devo” branches, and cognitive science, especially perceptual psychology and robotics. I trace the history of this question to the late 19th century, and through the conceptual revolutions of the 20th century. I show how the increasing interdisciplinary focus on the process of extracting information from an environment provides an opportunity for conceptual unification, and sketch an outline of what such a unification might look like.